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klebgenomics / Kleborate

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BiopythonDeprecationWarning error when running Kleborate. #46

Closed marjorie2205 closed 4 years ago

marjorie2205 commented 4 years ago

Hi, I am trying to run Kleborate but getting an error:

/home/ubuntu/miniconda3/lib/python3.7/site-packages/Bio/SubsMat/init.py:131: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module. BiopythonDeprecationWarning, Traceback (most recent call last): File "/home/ubuntu/miniconda3/bin/kleborate", line 33, in sys.exit(load_entry_point('Kleborate==0.4.0b0', 'console_scripts', 'kleborate')()) File "/home/ubuntu/miniconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 488, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/home/ubuntu/miniconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 2872, in load_entry_point return ep.load() File "/home/ubuntu/miniconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 2472, in load return self.resolve() File "/home/ubuntu/miniconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 2478, in resolve module = import(self.module_name, fromlist=['name'], level=0) File "/home/ubuntu/miniconda3/lib/python3.7/site-packages/kleborate/kleborate.py", line 28, in from .resBLAST import read_class_file, get_res_headers, resblast_one_assembly File "/home/ubuntu/miniconda3/lib/python3.7/site-packages/kleborate/resBLAST.py", line 25, in from .truncation import truncation_check File "/home/ubuntu/miniconda3/lib/python3.7/site-packages/kleborate/truncation.py", line 16, in from Bio.Alphabet import IUPAC File "/home/ubuntu/miniconda3/lib/python3.7/site-packages/Bio/Alphabet/init.py", line 21, in "Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information." ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

I see someone has reported this in #45 and they found that downgrading Biopython just gave a different error.

Grateful for guidance, thanks.

kelwyres commented 4 years ago

Hi Majorie, We've just done a new release (Kleborate v2.0.0), which has lots of new features and includes a fix for this problem. Please give it a try and let us know how you go. Thanks, Kelly

marjorie2205 commented 4 years ago

Hi Kelly, it's fixed my error, and appears to be happily working through my assemblies. Many thanks, Marjorie